ABSTRACT ? PROJECT 1 This P01 renewal application is in response to RFA, HD-16-009 from the NICHD to determine the developmental mechanisms of human structural birth defects, which, for this proposal, is congenital heart disease. Approximately 60% of patients with 22q11.2 deletion syndrome (22q11.2DS) have congenital heart disease, mostly of the conotruncal type including aortic arch anomalies. We refer to these defects as conotruncal and related aortic arch anomalies, termed CTRDs. These are structural birth defects that have impact on the entire life of the patient. The expressivity of those affected is highly variable, in that some have severe intracardiac anomalies such as persistent truncus arteriosus or tetralogy of Fallot, while others have mild malformations such as isolated ventricular septal defects or right-sided aortic arch anomalies. We are interested in identifying genetic modifiers for 22q11.2DS. The 22q11.2DS is a model genomic disorder for which we have collected over 2,000 DNA samples from patients. Although it is a rare disorder, occurring in 1/4000 live births, our central hypothesis is that CTRDs in patients with 22q11.2DS and patients with non- syndromic CTRDs (NS-CTRDs; Project 2) share the same etiologic mechanisms during embryonic development. The cardiac outflow tract and pharyngeal arch arteries, affected in patients, form from progenitor cell populations that are within the early embryonic pharyngeal apparatus. The pharyngeal apparatus is a temporary embryological structure that is vulnerable to genetic insults. In the current P01, we discovered that genetic modifiers of CTRDs are complex and arise via the full spectrum of genetic variation. To lessen the challenge to make clear discoveries, we are taking advantages of our extensive gene expression profiling data from mouse models of 22q11.2DS in Project 3, to create a pharyngeal arch based interactive gene network termed the PA-INet. This network will be used to examine genetic data available from individuals with 22q11.2DS. We will additionally examine other gene-sets to test other relevant hypothesis as to the origin of congenital heart disease in humans. All the gene-sets will be kept organized in the Bio-analytic Core. In Project 1, we will take a focused gene-set approach to make discoveries using SNP-genotype microarrays (Aim 1), whole exome sequence (WES; Aim 2) and whole genome sequence (WGS; Aim 3) data from 22q11.2DS patients, along with application of new computational tools of analysis. By taking this approach, we will discover the complete repertoire of genetic variation that act as modifiers of 22q11-CTRDs for which will be compared with those for NS-CTRDs (Project 2). Since the genetics of CTRDs is complex, we believe our strategy, focusing on 22q11.2DS and developmental mechanisms, will make it possible to gain unique inroads into this important human structural birth defect.